Metagenomic Functional Potential Predicts Degradation Rates of a Model Organophosphorus Xenobiotic in Pesticide Contaminated Soils
Chemical contamination of natural and agricultural habitats is an increasing global problem and a major threat to sustainability and human health. Organophosphorus (OP) compounds are one major class of contaminant and can undergo microbial degradation, however, no studies have applied system-wide ec...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2018-02-01
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| Series: | Frontiers in Microbiology |
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| Online Access: | http://journal.frontiersin.org/article/10.3389/fmicb.2018.00147/full |
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| author | Thomas C. Jeffries Thomas C. Jeffries Smriti Rayu Uffe N. Nielsen Kaitao Lai Kaitao Lai Ali Ijaz Loic Nazaries Brajesh K. Singh Brajesh K. Singh |
| author_facet | Thomas C. Jeffries Thomas C. Jeffries Smriti Rayu Uffe N. Nielsen Kaitao Lai Kaitao Lai Ali Ijaz Loic Nazaries Brajesh K. Singh Brajesh K. Singh |
| author_sort | Thomas C. Jeffries |
| collection | DOAJ |
| description | Chemical contamination of natural and agricultural habitats is an increasing global problem and a major threat to sustainability and human health. Organophosphorus (OP) compounds are one major class of contaminant and can undergo microbial degradation, however, no studies have applied system-wide ecogenomic tools to investigate OP degradation or use metagenomics to understand the underlying mechanisms of biodegradation in situ and predict degradation potential. Thus, there is a lack of knowledge regarding the functional genes and genomic potential underpinning degradation and community responses to contamination. Here we address this knowledge gap by performing shotgun sequencing of community DNA from agricultural soils with a history of pesticide usage and profiling shifts in functional genes and microbial taxa abundance. Our results showed two distinct groups of soils defined by differing functional and taxonomic profiles. Degradation assays suggested that these groups corresponded to the organophosphorus degradation potential of soils, with the fastest degrading community being defined by increases in transport and nutrient cycling pathways and enzymes potentially involved in phosphorus metabolism. This was against a backdrop of taxonomic community shifts potentially related to contamination adaptation and reflecting the legacy of exposure. Overall our results highlight the value of using holistic system-wide metagenomic approaches as a tool to predict microbial degradation in the context of the ecology of contaminated habitats. |
| first_indexed | 2024-12-23T19:01:50Z |
| format | Article |
| id | doaj.art-c074c62018a04159b4ed73e6e3b066db |
| institution | Directory Open Access Journal |
| issn | 1664-302X |
| language | English |
| last_indexed | 2024-12-23T19:01:50Z |
| publishDate | 2018-02-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Microbiology |
| spelling | doaj.art-c074c62018a04159b4ed73e6e3b066db2022-12-21T17:34:42ZengFrontiers Media S.A.Frontiers in Microbiology1664-302X2018-02-01910.3389/fmicb.2018.00147309432Metagenomic Functional Potential Predicts Degradation Rates of a Model Organophosphorus Xenobiotic in Pesticide Contaminated SoilsThomas C. Jeffries0Thomas C. Jeffries1Smriti Rayu2Uffe N. Nielsen3Kaitao Lai4Kaitao Lai5Ali Ijaz6Loic Nazaries7Brajesh K. Singh8Brajesh K. Singh9School of Science and Health, Western Sydney University, Penrith, NSW, AustraliaHawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, AustraliaHawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, AustraliaHawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, AustraliaHawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, AustraliaHealth and Biosecurity, Commonwealth Scientific and Industrial Research Organisation, North Ryde, NSW, AustraliaHawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, AustraliaHawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, AustraliaHawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, AustraliaGlobal Centre for Land Based Innovation, Western Sydney University, Penrith, NSW, AustraliaChemical contamination of natural and agricultural habitats is an increasing global problem and a major threat to sustainability and human health. Organophosphorus (OP) compounds are one major class of contaminant and can undergo microbial degradation, however, no studies have applied system-wide ecogenomic tools to investigate OP degradation or use metagenomics to understand the underlying mechanisms of biodegradation in situ and predict degradation potential. Thus, there is a lack of knowledge regarding the functional genes and genomic potential underpinning degradation and community responses to contamination. Here we address this knowledge gap by performing shotgun sequencing of community DNA from agricultural soils with a history of pesticide usage and profiling shifts in functional genes and microbial taxa abundance. Our results showed two distinct groups of soils defined by differing functional and taxonomic profiles. Degradation assays suggested that these groups corresponded to the organophosphorus degradation potential of soils, with the fastest degrading community being defined by increases in transport and nutrient cycling pathways and enzymes potentially involved in phosphorus metabolism. This was against a backdrop of taxonomic community shifts potentially related to contamination adaptation and reflecting the legacy of exposure. Overall our results highlight the value of using holistic system-wide metagenomic approaches as a tool to predict microbial degradation in the context of the ecology of contaminated habitats.http://journal.frontiersin.org/article/10.3389/fmicb.2018.00147/fullmetagenomicsbioremediationpesticidessoil microbiologybiodegradationenvironmental |
| spellingShingle | Thomas C. Jeffries Thomas C. Jeffries Smriti Rayu Uffe N. Nielsen Kaitao Lai Kaitao Lai Ali Ijaz Loic Nazaries Brajesh K. Singh Brajesh K. Singh Metagenomic Functional Potential Predicts Degradation Rates of a Model Organophosphorus Xenobiotic in Pesticide Contaminated Soils Frontiers in Microbiology metagenomics bioremediation pesticides soil microbiology biodegradation environmental |
| title | Metagenomic Functional Potential Predicts Degradation Rates of a Model Organophosphorus Xenobiotic in Pesticide Contaminated Soils |
| title_full | Metagenomic Functional Potential Predicts Degradation Rates of a Model Organophosphorus Xenobiotic in Pesticide Contaminated Soils |
| title_fullStr | Metagenomic Functional Potential Predicts Degradation Rates of a Model Organophosphorus Xenobiotic in Pesticide Contaminated Soils |
| title_full_unstemmed | Metagenomic Functional Potential Predicts Degradation Rates of a Model Organophosphorus Xenobiotic in Pesticide Contaminated Soils |
| title_short | Metagenomic Functional Potential Predicts Degradation Rates of a Model Organophosphorus Xenobiotic in Pesticide Contaminated Soils |
| title_sort | metagenomic functional potential predicts degradation rates of a model organophosphorus xenobiotic in pesticide contaminated soils |
| topic | metagenomics bioremediation pesticides soil microbiology biodegradation environmental |
| url | http://journal.frontiersin.org/article/10.3389/fmicb.2018.00147/full |
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